Salt‐Treated Roots of Oryza australiensis Seedlings are Enriched with Proteins Involved in Energetics and Transport

Salinity is a major constraint on rice productivity worldwide. However, mechanisms of salt tolerance in wild rice relatives are unknown. Root microsomal proteins are extracted from two Oryza australiensis accessions contrasting in salt tolerance. Whole roots of 2‐week‐old seedlings are treated with 80 mM NaCl for 30 days to induce salt stress. Proteins are quantified by tandem mass tags (TMT) and triple‐stage Mass Spectrometry. More than 200 differentially expressed proteins between the salt‐treated and control samples in the two accessions (p‐value <0.05) are found. Gene Ontology (GO) analysis shows that proteins categorized as “metabolic process,” “transport,” and “transmembrane transporter” are highly responsive to salt treatment. In particular, mitochondrial ATPases and SNARE proteins are more abundant in roots of the salt‐tolerant accession and responded strongly when roots are exposed to salinity. mRNA quantification validated the elevated protein abundances of a monosaccharide transporter and an antiporter observed in the salt‐tolerant genotype. The importance of the upregulated monosaccharide transporter and a VAMP‐like protein by measuring salinity responses of two yeast knockout mutants for genes homologous to those encoding these proteins in rice are confirmed. Potential new mechanisms of salt tolerance in rice, with implications for breeding of elite cultivars are also discussed.     

First fungus gnats of genus Manota Williston (Diptera: Mycetophilidae) from Japan

The genus Manota is recorded from Japan for the first time. Three new species, Manota satoyamanis, Manota indahae and Manota tunoae spp. nov., are described, based on specimens collected in an ecological sampling program of arthropods in the “satoyama” landscape of Ishikawa Prefecture. “Satoyama” represents the traditional rural landscape of Japan, which is characterized by a mosaic of secondary forests, plantations, ponds and rice paddy fields. The new species raise the number of Palearctic Manota species from five to eight.     

Glucocorticoid‐transactivated TSC22D3 attenuates hypoxia‐ and diabetes‐induced Müller glial galectin‐1 expression via HIF‐1α destabilization

Galectin‐1/LGALS1, a newly recognized angiogenic factor, contributes to the pathogenesis of diabetic retinopathy (DR). Recently, we demonstrated that glucocorticoids suppressed an interleukin‐1β‐driven inflammatory pathway for galectin‐1 expression in vitro and in vivo. Here, we show glucocorticoid‐mediated inhibitory mechanism against hypoxia‐inducible factor (HIF)‐1α‐involved galectin‐1 expression in human Müller glial cells and the retina of diabetic mice. Hypoxia‐induced increases in galectin‐1/LGALS1 expression and promoter activity were attenuated by dexamethasone and triamcinolone acetonide in vitro. Glucocorticoid application to hypoxia‐stimulated cells decreased HIF‐1α protein, but not mRNA, together with its DNA‐binding activity, while transactivating TSC22 domain family member (TSC22D)3 mRNA and protein expression. Co‐immunoprecipitation revealed that glucocorticoid‐transactivated TSC22D3 interacted with HIF‐1α, leading to degradation of hypoxia‐stabilized HIF‐1α via the ubiquitin‐proteasome pathway. Silencing TSC22D3 reversed glucocorticoid‐mediated ubiquitination of HIF‐1α and subsequent down‐regulation of HIF‐1α and galectin‐1/LGALS1 levels. Glucocorticoid treatment to mice significantly alleviated diabetes‐induced retinal HIF‐1α and galectin‐1/Lgals1 levels, while increasing TSC22D3 expression. Fibrovascular tissues from patients with proliferative DR demonstrated co‐localization of galectin‐1 and HIF‐1α in glial cells partially positive for TSC22D3. These results indicate that glucocorticoid‐transactivated TSC22D3 attenuates hypoxia‐ and diabetes‐induced retinal glial galectin‐1/LGALS1 expression via HIF‐1α destabilization, highlighting therapeutic implications for DR in the era of anti‐vascular endothelial growth factor treatment.     

drr‐2 encodes an eIF4H that acts downstream of TOR in diet‐restriction‐induced longevity of C. elegans

Dietary restriction (DR) results in a robust increase in lifespan while maintaining the physiology of much younger animals in a wide range of species. Here, we examine the role of drr‐2, a DR‐responsive gene recently identified, in determining the longevity of Caenorhabditis elegans. Inhibition of drr‐2 has been shown to increase longevity. However, the molecular mechanisms by which drr‐2 influences longevity remain unknown. We report here that drr‐2 encodes an ortholog of human eukaryotic translation initiation factor 4H (eIF4H), whose function is to mediate the initiation step of mRNA translation. The molecular function of DRR‐2 is validated by the association of DRR‐2 with polysomes and by the decreased rate of protein synthesis observed in drr‐2 knockdown animals. Previous studies have also suggested that DR might trigger a regulated reduction in drr‐2 expression to initiate its longevity response. By examining the effect of increasing drr‐2 expression on DR animals, we find that drr‐2 is essential for a large portion of the longevity response to DR. The nutrient‐sensing target of rapamycin (TOR) pathway has been shown to mediate the longevity effects of DR in C. elegans. Results from our genetic analyses suggest that eIF4H/DRR‐2 functions downstream of TOR, but in parallel to the S6K/PHA‐4 pathway to mediate the lifespan effects of DR. Together, our findings reveal an important role for eIF4H/drr‐2 in the TOR‐mediated longevity responses to DR.     

RNase H eliminates R‐loops that disrupt DNA replication but is nonessential for efficient DSB repair

In Saccharomyces cerevisiae, genome stability depends on RNases H1 and H2, which remove ribonucleotides from DNA and eliminate RNA–DNA hybrids (R‐loops). In Schizosaccharomyces pombe, RNase H enzymes were reported to process RNA–DNA hybrids produced at a double‐strand break (DSB) generated by I‐PpoI meganuclease. However, it is unclear if RNase H is generally required for efficient DSB repair in fission yeast, or whether it has other genome protection roles. Here, we show that S. pombe rnh1? rnh201? cells, which lack the RNase H enzymes, accumulate R‐loops and activate DNA damage checkpoints. Their viability requires critical DSB repair proteins and Mus81, which resolves DNA junctions formed during repair of broken replication forks. “Dirty” DSBs generated by ionizing radiation, as well as a “clean” DSB at a broken replication fork, are efficiently repaired in the absence of RNase H. RNA–DNA hybrids are not detected at a reparable DSB formed by fork collapse. We conclude that unprocessed R‐loops collapse replication forks in rnh1? rnh201? cells, but RNase H is not generally required for efficient DSB repair.     

Sequence polymorphisms in wild,weedy, and cultivated rice suggest seed‐shattering locus sh4 played a minor role in Asian rice domestication

The predominant view regarding Asian rice domestication is that the initial origin of nonshattering involved a single gene of large effect, specifically, the sh4 locus via the evolutionary replacement of a dominant allele for shattering with a recessive allele for reduced shattering. Data have accumulated to challenge this hypothesis. Specifically, a few studies have reported occasional seed‐shattering plants from populations of the wild progenitor of cultivated rice (Oryza rufipogon complex) being homozygous for the putative “nonshattering” sh4 alleles. We tested the sh4 hypothesis for the domestication of cultivated rice by obtaining genotypes and phenotypes for a diverse set of samples of wild, weedy, and cultivated rice accessions. The cultivars were fixed for the putative “nonshattering” allele and nonshattering phenotype, but wild rice accessions are highly polymorphic for the putative “nonshattering” allele (frequency ~26%) with shattering phenotype. All weedy rice accessions are the “nonshattering” genotype at the sh4 locus but with shattering phenotype. These data challenge the widely accepted hypothesis that a single nucleotide mutation (“G”/“T”) of the sh4 locus is the major driving force for rice domestication. Instead, we hypothesize that unidentified shattering loci are responsible for the initial domestication of cultivated rice through reduced seed shattering.     

Preferences Predict Food Intake From 5 to 11 Years,but Not in Girls With Higher Weight Concerns,Dietary Restraint,and %Body Fat

Food preferences (FP) predict food intake in childhood; however, the predictive power of FP may decline among girls as weight concerns (WC) and dietary restraint (DR) increase during preadolescence. To examine longitudinal change in the preference‐intake (P‐I) relation and assess whether this relation weakens among non‐Hispanic white girls (n = 197) with a history of WC and DR from age 5 to 11. Girls' preferences for and intake (kcal) of 10 palatable snack foods were assessed biennially. Height, weight, percent body fat (%BF), WC, and DR were measured. Individual correlation coefficients were calculated per girl to capture within‐person P‐I correlations at each time of measurement. Overall, FP predicted girls' snack food calorie intakes between 5 and 11 years, but latent profile analysis (LPA) revealed three distinct patterns of change in P‐I correlations over time: “strong/stable” P‐I correlations were relatively high and became stronger with age; “increasing/later null” P‐I correlations were initially weak and became stronger between 5 and 9 years, but dropped to near 0 at 11 years; “initially weak/later strong” P‐I correlations were initially null and increased with age. Mixed models revealed that the “increasing/later null” group had greater increases in %BF, and higher WC, DR, and BMI percentiles from 5 to 11 years, compared to the other groups. In summary, FP predicted snack food calorie intake among most girls during childhood, but waned as a predictor of calorie intake at age 11 for a subset of girls with increasing %BF, and higher WC, DR, and BMIs.     

A biogeographic–ecological approach to disentangle reticulate evolution in the Triatoma phyllosoma species group (Heteroptera: Triatominae), vectors of Chagas disease

Introgression and incomplete lineage sorting (ILS) are two of the main sources of gene‐tree incongruence; both can confound the assessment of phylogenetic relationships among closely related species. The Triatoma phyllosoma species group is a clade of partially co‐distributed and cross‐fertile Chagas disease vectors. Despite previous efforts, the phylogeny of this group remains unresolved, largely because of substantial gene‐tree incongruence. Here, we sequentially address introgression and ILS to provide a robust phylogenetic hypothesis for the T. phyllosoma species group. To identify likely instances of introgression prior to molecular scrutiny, we assessed biogeographic data and information on fertility of inter‐specific crosses. We first derived a few explicit hybridization hypotheses by considering the degree of spatial overlap within each species pair. Then, we assessed the plausibility of these hypotheses in the light of each species pair's cross‐fertility. Using this contextual information, we evaluated mito‐nuclear (cyt b, ITS‐2) gene‐tree incongruence and found evidence suggesting introgression within two species pairs. Finally, we modeled ILS using a Bayesian multispecies coalescent approach and either (a) a “complete” dataset with all the specimens in our sample, or (b) a “filtered” dataset without putatively introgressed specimens. The “filtered tree” had higher posterior‐probability support, as well as more plausible topology and divergence times, than the “complete tree.” Detecting and filtering out introgression and modeling ILS allowed us to derive an improved phylogenetic hypothesis for the T. phyllosoma species group. Our results illustrate how biogeographic and ecological‐reproductive contextual information can help clarify the systematics and evolution of recently diverged taxa prone to introgression and ILS.     

EFFECT OF VARIETAL DIFFERENCES AND POLISHING OF RICE ON QUALITY PARAMETERS OF IDLI

The effect of varietal differences and polishing of rice on quality parameters of “idli,” an Indian fermented product, were studied. In addition, the functional properties of decorticated (whole and split) black gram (Phaseolus mungo Roxb.), were also determined. Two varieties of raw rice, “Jaya” and “Minilong,” and one variety of parboiled rice “Ponni” with two degrees of polishing (high and low) were selected. Idlis were prepared following standard procedures. Variations were observed in water and fat absorption capacities of two black gram samples. Emulsification capacity ranged from 102 to 110 mL/100 g. Foam capacities at different pH range were similar, but foam stability differed as a function of time. The pH of the fermented batter was between 4.1 and 4.8. Rice with a lesser degree of polishing fermented better with higher batter volume and microbial count, lesser shear value and gave softer idlis. However, sensory analysis revealed that idlis prepared with low‐polish rice scored significantly lower for appearance and color quality compared with products prepared with high‐polish rice. Significant differences were observed in the quality of flavor of all products. It can be concluded that the quality characteristics of Idli were influenced by the variety of rice and the degree of polishing, but the two types of black gram used, whole and split, had no effect.     

Helicobacter pylori outer inflammatory protein A (OipA) suppresses apoptosis of AGS gastric cells in vitro

Outer inflammatory protein A (OipA) is an important virulence factor associated with gastric cancer and ulcer development; however, the results have not been well established and turned out to be controversial. This study aims to elucidate the role of OipA in Helicobacter pylori infection using clinical strains harbouring oipA “on” and “off” motifs. Proteomics analysis was performed on AGS cell pre‐infection and postinfection with H. pylori oipA “on” and “off” strains, using liquid chromatography/mass spectrometry. AGS apoptosis and cell cycle assays were performed. Moreover, expression of vacuolating cytotoxin A (VacA) was screened using Western blotting. AGS proteins that have been suggested previously to play a role or associated with gastric disease were down‐regulated postinfection with oipA “off” strains comparing to oipA “on” strains. Furthermore, oipA “off” and ΔoipA cause higher level of AGS cells apoptosis and G0/G1 cell‐cycle arrest than oipA “on” strains. Interestingly, deletion of oipA increased bacterial VacA production. The capability of H. pylori to induce apoptosis and suppress expression of proteins having roles in human disease in the absence of oipA suggests that strains not expressing OipA may be less virulent or may even be protective against carcinogenesis compared those expressing OipA. This potentially explains the higher incidence of gastric cancer in East Asia where oipA “on” strains predominates.     

Molecular characterization,spatial‐temporal expression and magnetic response patterns of iron‐sulfur cluster assembly1 (IscA1) in the rice planthopper,Nilaparvata lugens

The mechanisms of magnetoreception have been proposed as the magnetitebased, the chemical radical-pair and biocompass model, in which magnetite particles, the cryptochrome (Cry) or iron-sulfur cluster assembly 1 (IscA1) may be involved. However, little is known about the association among the molecules. Here we investigated the molecular characterization and the mRNA expression of IscA1 in different developmental stages, tissues and magnetic fields in the migratory brown planthopper (BPH), Nilaparvata lugens. NlIscA1 contains an open reading frame of 390 bp, encoding amino acids of 129, with the predicted molecular weight of 14.0 kDa and the isoelectric point of 9.10. Well-conserved Fe-S cluster binding sites were observed in the predicted protein. Phylogenetic analysis demonstrated NlIscA1 to be clustered into the insect's IscA1. NlIscA1 showed up-regulated mRNA expression during the period of migration. The mRNA expression of NlIscA1 could be detected in all the three tissues of head, thorax and abdomen, with the highest expression level in the abdomen. For the macropterous migratory Nilaparvata lugens, mRNA expression of NlIscA1 and N. lugens cryptochromel (Nlcry1) were up-regulated under the magnetic fields of 5 Gauss and 10 Gauss in strength (vs. local geomagnetic field), while N. lugens cryptochrome 2 (Nlcry2) remained stable. For the brachyterous non-migratory Nilaparvata lugens, no significant changes were found in mRNA expression of NlIscA1, Nlcry1 and Nlcry2 among different magnetic fields. These findings preliminarily reveal that the expression of NlIscA1 and Nlcry1 exhibited coordinated responses to the magnetic field. It suggests some potential associations among the putative magneto-sensitive molecules of cryptochrome and iron-sulfur cluster assembly.     

MiR‐129‐5p promotes docetaxel resistance in prostate cancer by down‐regulating CAMK2N1 expression

This study focuses on the effect of miR‐129‐5p on docetaxel‐resistant (DR) prostate cancer (PCa) cells invasion, migration and apoptosis. In our study, the expression of CAMK2N1 was assessed by qRT‐PCR in PCa patient tissues and cell lines including PC‐3 and PC‐3‐DR. Cells transfected with miR‐129‐5p mimics, inhibitor, CAMK2N1 or negative controls (NC) were used to interrogate their effects on DR cell invasions, migrations and apoptosis during docetaxel (DTX) treatments. The apoptosis rate of the PCa cells was validated by flow cytometry. Relationships between miR‐129‐5p and CAMK2N1 levels were identified by qRT‐PCR and dual‐luciferase reporter assay. CAMK2N1 was found to be down‐expressed in DR PCa tissue sample, and low levels of CAMK2N1 were correlated with high docetaxel resistance and clinical prediction of poor survival. CAMK2N1 levels were decreased in DR PCa cells treated with DXT. We further explored that up‐regulation of miR‐129‐5p could promote DR PCa cells viability, invasion and migration but demote apoptosis. Involved molecular mechanism studies revealed that miR‐129‐5p reduced downstream CAMK2N1 expression to further impact on chemoresistance to docetaxel of PCa cells, indicating its vital role in PCa docetaxel resistance. Our findings revealed that miR‐129‐5p contributed to the resistance of PC‐3‐DR cells to docetaxel through suppressing CAMK2N1 expression, and thus targeting miR‐129‐5p may provide a novel therapeutic approach in sensitizing PCa to future docetaxel treatment.     

The field-dependence of the solid-state photo-CIDNP effect in two states of heliobacterial reaction centers

The solid-state photo-CIDNP (photochemically induced dynamic nuclear polarization) effect is studied in photosynthetic reaction centers of Heliobacillus mobilis at different magnetic fields by ¹³C MAS (magic-angle spinning) NMR spectroscopy. Two active states of heliobacterial reaction centers are probed: an anaerobic preparation of heliochromatophores (“Braunstoff”, German for “brown substance”) as well as a preparation of cells after exposure to oxygen (“Grünstoff”, “green substance”). Braunstoff shows significant increase of enhanced absorptive (positive) signals toward lower magnetic fields, which is interpreted in terms of an enhanced differential relaxation (DR) mechanism. In Grünstoff, the signals remain emissive (negative) at two fields, confirming that the influence of the DR mechanism is comparably low.     

Differential Sensitivity of Macrocarpa and Microcarpa Types of Chickpea （Cicer arietinum L.） to Water Stress： Association of Contrasting Stress Response with Oxidative Injury

Chickpea (Cicer arietinum L.) is particularly sensitive to water stress at its reproductive phase and, under conditions of water stress, will abort flowers and pods, thus reducing yield potential. There are two types of chickpea: (i) Macrocarpa (“Kabuli”), which has large, rams head‐shaped, light brown seeds; and (ii) Microcarpa (“Desi”), which has small, angular and dark‐brown seeds. Relatively speaking, “Kabuli” has been reported to be more sensitive to water stress than “Desi”. The underlying mechanisms associated with contrasting sensitivity to water stress at the metabolic level are not well understood. We hypothesized that one of the reasons for contrasting water stress sensitivity in the two types of chickpea may be a variation in oxidative injury. In the present study, plants of both types were water stressed at the reproductive stage for 14 d. As a result of the stress, the “Kabuli” type exhibited an 80% reduction in seed yield over control compared with a 64% reduction observed for the “Desi” type. The decrease in leaf water potential (Ψ_w) was faster in the “Kabuli” compared with the “Desi” type. At the end of the water stress period, Ψ_w was reduced to ?2.9 and ?3.1 MPa in the “Desi” and “Kabuli” types, respectively, without any significant difference between them. On the last day of stress, “Kabuli” experienced 20% more membrane injury than “Desi”. The chlorophyll content and photosynthetic rate were significantly greater in “Desi” compared with “Kabuli”. The malondialdehyde and H₂O₂ content were markedly higher at the end of the water stress in “Kabuli” compared with “Desi”, indicating greater oxidative stress in the former. Levels of anti‐oxidants, such as ascorbic acid and glutathione, were significantly higher in “Desi” than “Kabuli”. Superoxide dismutase and catalase activity did not differ significantly between the two types of chickpea, whereas on the 10th day, the activities of ascorbate peroxidase, dehydroascorbate reductase, and glutathione reductase were higher in “Desi”. These findings indicate that the greater stress tolerance in the “Desi” type may be ascribed to its superior ability to maintain better water status, which results in less oxidative damage. In addition, laboratory studies conducted by subjecting both types of chickpea to similar levels of polyethylene glycol‐induced water stress and to 10 μ.mol/L abscisic acid indicated a greater capacity of the “Desi” type to deal with oxidative stress than the “Kabuli” type. (Managing editor: Ping He)     

Structures of Arg‐ and Gln‐type bacterial cysteine dioxygenase homologs

In some bacteria, cysteine is converted to cysteine sulfinic acid by cysteine dioxygenases (CDO) that are only ～15–30% identical in sequence to mammalian CDOs. Among bacterial proteins having this range of sequence similarity to mammalian CDO are some that conserve an active site Arg residue (“Arg‐type” enzymes) and some having a Gln substituted for this Arg (“Gln‐type” enzymes). Here, we describe a structure from each of these enzyme types by analyzing structures originally solved by structural genomics groups but not published: a Bacillus subtilis “Arg‐type” enzyme that has cysteine dioxygenase activity (BsCDO), and a Ralstonia eutropha “Gln‐type” CDO homolog of uncharacterized activity (ReCDOhom). The BsCDO active site is well conserved with mammalian CDO, and a cysteine complex captured in the active site confirms that the cysteine binding mode is also similar. The ReCDOhom structure reveals a new active site Arg residue that is hydrogen bonding to an iron‐bound diatomic molecule we have interpreted as dioxygen. Notably, the Arg position is not compatible with the mode of Cys binding seen in both rat CDO and BsCDO. As sequence alignments show that this newly discovered active site Arg is well conserved among “Gln‐type” CDO enzymes, we conclude that the “Gln‐type” CDO homologs are not authentic CDOs but will have substrate specificity more similar to 3‐mercaptopropionate dioxygenases.